github.com/OpenMS/OpenMS commits | Ecosyste.ms: OpenCollective

added TOPP FLASHDeconv tool test

1f1e312a4fd2b475be9ab29e9b3f121263ce5c42 authored over 3 years ago by JeeH-K <[email protected]>

Update knime_package_support.cmake

077bda2e88c01d0d03dac57b992a26d9bd9a09ce authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Try to also copy the OpenMS libs themselves

Somehow CMake just stopped doing it...

4bb967c8f477b5bb2a5dc1e3da633d30efc6050c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update PythonExtensionChecker.py (#5433)

* [FIX] test_DIAScoring.py (#5432)

* Update PythonExtensionChecker.py

change what() to get...

84b5bf2d54424be1b81ce28724fcfc6386e94070 authored over 3 years ago by axelwalter <[email protected]>

[FIX] test_DIAScoring.py (#5432)

ab4f3718cae4b24301b3b214e84a98a7e58d532f authored over 3 years ago by Oliver Alka <[email protected]>

[FIX] compiler warnings (#5425)

578ad42ce4b58f84c41d26025a30ddae2cf0b253 authored over 3 years ago by Oliver Alka <[email protected]>

added missing ion names (#5426)

933fdbeba9ec1d5b2e05ef6970202628f0a3620e authored over 3 years ago by Timo Sachsenberg <[email protected]>

added changed params using script on Linux (bash works), added small … (#5427)

* added changed params using script on Linux (bash works), added small workaround for current do...

ee1392beb26e4a81601b289ae314712163afd6ce authored over 3 years ago by Timo Sachsenberg <[email protected]>

Update AUTHORS (#5428)

da6d087f73d232e959290455eb693927c91c88f6 authored over 3 years ago by Timo Sachsenberg <[email protected]>

update rest server helper script to exclude new GUI tools (#5429)

Co-authored-by: timosachsenberg <[email protected]>

e5de580400ebdf238b1241c306f41468b44c4305 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Changelog: main features (#5424)

* main features

* Update CHANGELOG

* Update CH...

e83be6e9a6df6e6ba84fe8546be42d8e93ed33a4 authored over 3 years ago by Timo Sachsenberg <[email protected]>

Merge pull request #5430 from OpenMS/axelwalter-patch-1

Update CMakeLists.txt

d5f27edb1f448cd24a5ab2c69dddbaf572114af8 authored over 3 years ago by axelwalter <[email protected]>

Update CMakeLists.txt

whitelist "version" in mzQC file

c9c3366fe82f3b5947f256e7a61cbabb691170b7 authored over 3 years ago by axelwalter <[email protected]>

Feature/ubuntu warnings (#5422)

* remove PERL_PATH from Doxyfile.in

* remove MSCGEN_PATH from Doxyfile.in

* remove PERL an...

7d774719ba0506190fac66e92fd2147542116e56 authored over 3 years ago by axelwalter <[email protected]>

change the year number

0dd6c91506b26ba377ed005b3a876d28a06ffd8f authored over 3 years ago by JeeH-K <[email protected]>

change the version number and added the script for it

5d28a13bac1f4911b4d49012343ff5c0ec442be0 authored over 3 years ago by JeeH-K <[email protected]>

Merge branch 'develop' of https://github.com/oliveralka/OpenMS into develop

7700fd424b0ecd4078d55e4c784e0cdba3f83e87 authored over 3 years ago by oliveralka <[email protected]>

Merge remote-tracking branch 'upstream/develop' into develop

a10ae614bd384150146cee50511a2770a84b7629 authored over 3 years ago by oliveralka <[email protected]>

Code Arrangement changes #3 (#5420)

* Code Arrangement changes #3

* Update PrecursorIonSelectionPreprocessing.cpp

* change in ...

28b1a58ca55a623a72336e374a3e2eeaefe9c893 authored over 3 years ago by Aman Kumar <[email protected]>

Merge remote-tracking branch 'upstream/develop' into develop

bc5664a5f873c98a84b348ad620bae1a898bac10 authored over 3 years ago by oliveralka <[email protected]>

Merge branch 'develop' of https://github.com/oliveralka/OpenMS into develop

ad82037398e2ad7e457a66068dea502a0f245bf0 authored over 3 years ago by oliveralka <[email protected]>

FLASHDeconv bruker testing

05b94c4871715ce61cf09e4d56a6d32bb4f6379e authored over 3 years ago by kyowonjeong <[email protected]>

Style changes (#5415)

83b1f9d3e3949963eaa0d3e01b9a96a504d249fd authored over 3 years ago by Oliver Alka <[email protected]>

[ADD] Docstring example for digestUnmodified (#5418)

* add example digestUnmodified

498b2b8441b20bae5272735fbf5daddd46c81e91 authored over 3 years ago by Oliver Alka <[email protected]>

remove unused parameter (#5417)

050acbf92480b135f93fc889adfddf61420a0e7a authored over 3 years ago by Timo Sachsenberg <[email protected]>

[FIX] Add inheritance to enzyme python wrappers (#5396)

* add inheritance

* fix wrap-doc

* FIX inherited functions

* FIX typo

* Add req chan...

6a0f9a45c4c8a18e070751d21ea5738abb4b0051 authored over 3 years ago by Oliver Alka <[email protected]>

Merge remote-tracking branch 'upstream/develop' into develop

1b570bcec4d5a123f356343a9bc1196ecddef921 authored over 3 years ago by oliveralka <[email protected]>

[Update] SIRIUS to 4.9.0 (#5409)

* Update SIRIUS to 4.9.0

* THIRDPARTY master

* change inline; fix test

a4496d90cf4f1a46218d55994db99e658fd9414d authored over 3 years ago by Oliver Alka <[email protected]>

Added wrap-doc methods #4 (#5407)

* Added wrap-doc methods

5d9d9b88a9d0e06803f404f3b6ea957ab8bbdbda authored over 3 years ago by Rahul Agrawal <[email protected]>

Added subscores for pepXML to idXML conversion// MSFragger Open search features (#5360)

* Added subscores for pepXML to idXML conversion

* MSFragger support in Percolatoradapter &
...

6b9111a7f93d420f8f6b30b6a4106f85896697b0 authored over 3 years ago by tillenglert <[email protected]>

Merge pull request #5414 from OpenMS/feature/mzqc_cv

update CV URL

de98a2732c3ca19f31beef3c9c0854c088009ab6 authored over 3 years ago by axelwalter <[email protected]>

update CV URL

6ef38fe59776d6f83fd319542c54a2553063ae85 authored over 3 years ago by axelwalter <[email protected]>

Merge branch 'develop' of https://github.com/oliveralka/OpenMS into develop

35fac51421847438969a61f648e8e3feed9f53c6 authored over 3 years ago by oliveralka <[email protected]>

FLASHDeconv bruker testing

22d5d0e2b69f19289b54ff1896d0a00ea816e8a2 authored over 3 years ago by kyowonjeong <[email protected]>

FLASHDeconv bruker testing

8c6c2dc0afdc3ce35365b047dc2dfe8505440a8b authored over 3 years ago by kyowonjeong <[email protected]>

Merge pull request #5392 from OpenMS/feature/mzqc_export

Feature/mzqc export

1a93d9cc125d8df3b32b720f5dd7151ee8abf61c authored over 3 years ago by axelwalter <[email protected]>

Update src/openms/include/OpenMS/FORMAT/QcMLFile.h

Co-authored-by: Timo Sachsenberg <[email protected]>

db82a7fe089440acf4cf5d752d9f1392c9263f6b authored over 3 years ago by axelwalter <[email protected]>

Update src/openms/include/OpenMS/FORMAT/QcMLFile.h

Co-authored-by: Timo Sachsenberg <[email protected]>

ee9a815ee7a225e8497d431425af2d42c4f91132 authored over 3 years ago by axelwalter <[email protected]>

add missing include to QcMLFile

acce4ff3c351b1f74cf57c273f16631f3bf907aa authored over 3 years ago by axelwalter <[email protected]>

clean up includes

e33b91bd38785bacb665b538484d7a61f4b24b88 authored over 3 years ago by axelwalter <[email protected]>

qcml export takes in memory data

b082030ae784271f778ad4a7f6b3ba837d637303 authored over 3 years ago by axelwalter <[email protected]>

Added wrap-doc method #3 (#5397)

* added wrap-doc method

* Update src/pyOpenMS/pxds/CVMappings.pxd

Co-authored-by: Oliver A...

930b5b881bdf531ab0cb295c9fecd1b7eefe5423 authored over 3 years ago by Rahul Agrawal <[email protected]>

mzqc export takes in memory data

401f729d25e5db4ef343bfc33fc8942ea5cfcd92 authored over 3 years ago by axelwalter <[email protected]>

Code Arrangement changes #2 (#5406)

Co-authored-by: Arraxx <[email protected]>

a146aed325d6afb64e6d622d39bcf6c4cefe6b8b authored over 3 years ago by Aman Kumar <[email protected]>

update test mzqc export

e8dce9b30f68743eccb834e4a8cab8b55ff5c4fe authored over 3 years ago by axelwalter <[email protected]>

fix small cp bug

caa4fae964f11ce766bf0e0549714f396ac1a364 authored over 3 years ago by Timo Sachsenberg <[email protected]>

rename getTIC to calculateTIC

65e6d104777ee48a082f15ee2db9e38b97cf5eca authored over 3 years ago by Timo Sachsenberg <[email protected]>

[REFACTOR] move FeatureFinderMetaboIdent code from tool to library (#5230)

* moved ffmetaboid to library

* fix typo

* Update FeatureFinderAlgorithmMetaboIdent.h

*...

60f38cdeeff20fb85259272399bf448b5d4a8af1 authored over 3 years ago by Timo Sachsenberg <[email protected]>

The initial Data visualization is complete using nightingale library

1e5aa74f75794de6ada7ae097153f29a1929b7df authored over 3 years ago by Dhanmoni Nath <[email protected]>

remove now unnecessary code to extract basename (#5393)

* remove now unnecessary code to extract basename

* replaced another occurance

355cc84f918e7f63cc9cd83569dfd51a18aea7ba authored over 3 years ago by Timo Sachsenberg <[email protected]>

Small Code Arrangement changes (#5405)

Co-authored-by: Arraxx <[email protected]>

32991d2d3c150f60ee837bee7f77ea8009681d32 authored over 3 years ago by Aman Kumar <[email protected]>

improvements in IdentificationSummary

48ecba06c39b091cbc2e03713150992b11378daf authored over 3 years ago by axelwalter <[email protected]>

simplify mean rt deviation calculation

28cd323bcc4d8eccfa977e1b257855d4b562e9c2 authored over 3 years ago by axelwalter <[email protected]>

MissedCleavages refactoring

38eb6672584d0927b81258edf7c2792cff805d15 authored over 3 years ago by axelwalter <[email protected]>

[FIX] Class tests memory leaks (#5390)

* [fix] Fix various memory leaks in tests

* Fix numerous memory leaks in tests

* [fix] Fix...

eff53eb5c73fb5971c190ab25bd36c2a3e673e01 authored over 3 years ago by David Voigt <[email protected]>

Correctly setup c17 for pyopenms (#5401)

5548dcf1262ce00aef64b62d574b190e8e7b2bf3 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

Update PULL_REQUEST_TEMPLATE.md

1b8c8a059b9f275a88eced93a6068a51f226a8cf authored over 3 years ago by Timo Sachsenberg <[email protected]>

rt mean calculation

7cfddb994016f08e936a8b80784a6ea980d52446 authored over 3 years ago by axelwalter <[email protected]>

annotate members

d6ef15e8b552c55b5af34ba32061790fa220b72f authored over 3 years ago by axelwalter <[email protected]>

compute functions don't read from file

c87e8d796deff8d38309a25dc48cd6f1ed99f390 authored over 3 years ago by axelwalter <[email protected]>

QWidget::grab() (#5394)

e1252f2fa6b24bd3843859914be7e132f9db79d6 authored over 3 years ago by Oliver Alka <[email protected]>

rename qc classes

1183ae4bc1c89ecf7516b1c3b5c39b0c26e986b1 authored over 3 years ago by axelwalter <[email protected]>

Improved docs in pxd's (#5382)

* annotations added

* files added

* files-added

* first-letter-capitalized

* Update ...

aedce62b780ff8089f413ee29e9f78d11b076144 authored over 3 years ago by Rahul Agrawal <[email protected]>

delete Elements.xml

94c9370cafa86578c8f249f45cb7afdd35d7d034 authored over 3 years ago by Timo Sachsenberg <[email protected]>

start and end position of peptide extracted

67af40af5c744637d628883689f3c4b70c2d197c authored over 3 years ago by Dhanmoni Nath <[email protected]>

protein sequence, accessions, peptide start, end, seq extracted and send to JS using QJsonDocument

d599f8ed36fd5833bca0f82b62228e8e15cf90c2 authored over 3 years ago by Dhanmoni Nath <[email protected]>

add peptide/protein identifications

7a0fff1f863a3207f7fe008e5f1bc7a93f19ba0b authored over 3 years ago by axelwalter <[email protected]>

new window appears on sequence clicked, and shows sequence inside html page

920247410e7e82d2ea2a67b5c8dfd0467f62ff42 authored over 3 years ago by Dhanmoni Nath <[email protected]>

Merge pull request #5385 from poshul/feature_moveconfig

[fix] updated the config storage path for linux

7b74d2c002aaf14c5bbfcc430ded009dc32cfb85 authored over 3 years ago by Samuel Wein <[email protected]>

[fix] fixed variable scoping goof.

0ff0d38c0bf440348fbfe41f0e258d13ceaeed0f authored over 3 years ago by Samuel Wein <[email protected]>

[fix] address reviewer comments

0b0216b4935375fea7ba1562decbf36b1e41fe5a authored over 3 years ago by Samuel Wein <[email protected]>

[fix] added support for explicitly specified XDG_CONFIG_HOME parameters

c5b7a32390ac358d3111f671e5893994ed2ebd7c authored over 3 years ago by Samuel Wein <[email protected]>

[fix] Added some additional logic to determine platform for tool names

34406e445f0057dc438e8aa8cb6899bf96839ea0 authored over 3 years ago by Samuel Wein <[email protected]>

merge TopFD output format checkboxes into one

2d6170ea59b098c2473a82a45f165fe998efe21d authored over 3 years ago by JeeH-K <[email protected]>

rename variables

59cb28de0bf3e81aaafcebe1a601fbc4919eaa95 authored over 3 years ago by axelwalter <[email protected]>

add RT shift mean and update qc-cv

6a32c1009e2d72f73b479c459a8bfb1ad927b692 authored over 3 years ago by axelwalter <[email protected]>

Merge pull request #5383 from cbielow/test_opt

Fix class test macro

66e8b4ebd8755193529b18a249440cc0dc50c54f authored over 3 years ago by Chris Bielow <[email protected]>

more fixes for CI

a6836d9a7762b03df29a2091df541b7d11daf546 authored over 3 years ago by bielow <[email protected]>

make exception for Windows (in a VM)

800313c0cbfcb8144e11c28f289d0c6994be828f authored over 3 years ago by bielow <[email protected]>

Merge pull request #5341 from bertrandboudaud/feature/TargetedSpectraExtractor_storeSpectra_for_pr

Feature/targeted spectra extractor store spectra for pr

47f08c48322b25e43d005616e3366e4265fea5d8 authored over 3 years ago by Julianus Pfeuffer <[email protected]>

some stopwatch debug stuff

b9f85a5b8d6346e28cea4e8631bd87b4872c64c8 authored over 3 years ago by bielow <[email protected]>

open new widget with sequence data when clicked on sequence of a row

000c9bcfe61b907d248dce0fb577296d7a09f6f0 authored over 3 years ago by Dhanmoni Nath <[email protected]>

aggressive fix

4c59eaaa99127183749c4dffdb32c4ba027b529a authored over 3 years ago by bielow <[email protected]>

open uniprot site on browser on accession clicked feature added

8e0aefc46ad8ddfa7ad9e1a689e0a1ef5cb86b6d authored over 3 years ago by Dhanmoni Nath <[email protected]>

attempt to fix StopWatch test

962645766f205aaf2a6c8eb8ea2df1d481fd9813 authored over 3 years ago by bielow <[email protected]>

fix test

9976d5a8b57c38983820a49b8f44d961b197f33f authored over 3 years ago by bielow <[email protected]>

Merge pull request #5386 from jpfeuffer/gnpsexport

[FEATURE] Rebased GNPSExport

4557880c2bf22327059549edf467c782ce9b590c authored over 3 years ago by Julianus Pfeuffer <[email protected]>

correct tool registry

1adcbe89c9f696139ac97b4324af33743e08dbb6 authored over 3 years ago by jpfeuffer <[email protected]>

[GNPSExport] Refactor code and address integration test errors

Deduped code between export types and simplified topp unit tests.
Also addressed Travis integrat...

3d6a336c34e8e3185dbe9fd16a43dc268ac190a1 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

fix/upd GNPSExport mem reading mzml files

8c672737c650dbfa41b463dc9503b858e1d50e18 authored over 3 years ago by Abi Sarvepalli <[email protected]>

upd GNPSExport test suite

c0865fe2011c50514b1b8673f8c1550cc99a7a8b authored over 3 years ago by Abi Sarvepalli <[email protected]>

upd test suite ini files

1e98c211d76c7b80164e1d448b848c034d562b42 authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix: trailing whitespaces and extra blank lines

12aee8d4ab777e2f17595e944e8a2559e4cf7c7d authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

upd GNPSExport mem management

f641f7e5e08ee735674d67bf0b3681386c975405 authored over 3 years ago by Abi Sarvepalli <[email protected]>

Addressed PR 4761 to OpenMS/openms

https://github.com/openms/openms/pull/4761

Added...
- Technical documentation to method headers
...

59c43b3dd1cc73678a54de61d8bc9bf569c94aa6 authored over 3 years ago by Abinesh Sarvepalli <[email protected]>

remove large test case

97b93b7c415a14d06e7694a7e9eff6639d649637 authored over 3 years ago by Abi Sarvepalli <[email protected]>

refactor write to file as method

bea1e5d463949e27ae8f0394110bdde6aabb5b1d authored over 3 years ago by Abi Sarvepalli <[email protected]>

refactor getSpectrumAtIndex -> getSpectraAtIndex

5e8815f557e982aa06992f69b113a725365e6d97 authored over 3 years ago by Abi Sarvepalli <[email protected]>

close output stream

5367d47bb24093d8fbf32f83547ada385555911f authored over 3 years ago by Abi Sarvepalli <[email protected]>

fix tool description

eb791aec4f21f9741e68248a485beb8ef30b7ca9 authored over 3 years ago by Abi Sarvepalli <[email protected]>